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spatstat (version 1.21-6)

Spatial Point Pattern analysis, model-fitting, simulation, tests

Description

A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. Contains over 1000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images and tessellations. Exploratory methods include K-functions, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

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Version

Install

install.packages('spatstat')

Monthly Downloads

16,590

Version

1.21-6

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

March 26th, 2011

Functions in spatstat (1.21-6)

Extract Subset of Image

Orientation Angles of Line Segments

Spherical Contact Distribution Function

ANOVA for Fitted Point Process Models

Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern

Diggle-Gratton model

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Concatenate x,y Coordinate Vectors

as.data.frame.im

Convert Pixel Image to Data Frame

Apply Affine Transformation To Point Pattern

Distance to Boundary of Window

Convert a Window to a Polygonal Window

Diagnostics for random marking

Apply Affine Transformation To Line Segment Pattern

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

K-function using FFT

Bounding Box of a Window or Point Pattern

Test Whether An Object Is A Point Pattern

Areas of Morphological Erosions

Ord's Interaction model

Test Whether An Object Is A Pixel Image

Marked J Function

Nearest neighbour distances between line segments

Morphological Dilation

Histogram of Pixel Values in an Image

Point Patterns of New Brunswick Forest Fires

Distance for a Point Pattern Matching

Stoyan's Rule of Thumb for Bandwidth Selection

Coefficients of Fitted Spatial Logistic Regression Model

Clark and Evans Aggregation Index

complement.owin

Take Complement of a Window

Interactively Add Points

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Weighted Empirical Cumulative Distribution Function

Log Likelihood for Poisson Point Process Model

Multitype J Function (i-to-j)

Print News About Latest Version of Package

Area of a Window

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Classify Points in a Point Pattern

Fitted Conditional Intensity for Point Process Model

Convert Data To Class owin

Inhomogeneous Multitype K Dot Function

Create a Function Value Table

Inhomogeneous K-function

Pair Correlation Function of a Three-Dimensional Point Pattern

Areas of Morphological Dilations

Poisson Point Process Model

Extract the Interaction from a Fitted Point Process Model

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Scatterplot Matrix for Pixel Images

Inhomogeneous Pair Correlation Function

Morphological Opening

clarkevans.test

Clark and Evans Test

Pairwise distances between two different line segment patterns

Estimate the I-function

Summarise Marks in Every Neighbourhood in a Point Pattern

Apply Affine Transformation

Beadlet Anemones Data

Test Whether Two Function Objects Are Compatible

Mosaic Random Set

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Determine Whether One Window is Contained In Another

Convert Pixel Image from Numeric to Factor

Perspective Plot of Pixel Image

Fit cluster point process model

Test Whether Two Pixel Images Are Compatible

Reset Values in Subset of Image

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Distance to Boundary of Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

quadratresample

Resample a Point Pattern by Resampling Quadrats

Inhomogeneous Multitype L Dot Function

Kaplan-Meier Estimator using Histogram Data

Convert Data to Three-Dimensional Box

Pairwise distances

Signed or Vector-Valued Measure

Nearest neighbours in three dimensions

Extract or Replace Subset of Point Pattern

Integral of a Pixel Image

Morphological Closing

Colour Lookup Tables

Class of Images

Multitype L-function (i-to-any)

Subdivide a Window or Tessellation using a Set of Lines

The Multitype Strauss Point Process Model

Distance Map of Line Segment Pattern

Murchison gold deposits

Print Brief Details of a Line Segment Pattern Dataset

Multitype pair correlation function (i-to-any)

Pairwise Distances in Any Dimensions

Compute Expansion Window for Simulation

The Hard Core Point Process Model

Evaluate Expression Involving Function Arrays

Distance Map of Point Pattern

Convert Window to Another Unit of Length

Kernel Smoothing of Line Segment Pattern

Kolmogorov-Smirnov Test for Point Process Model

Japanese Pines Point Pattern

Test whether Object is Multitype

Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)

Summarizing a Pixel Image

Pairwise distances between line segments

Intersection of Two Tessellations

Smoothing Estimate of Covariate Transformation

Ponderosa Pine Tree Point Pattern

Summarizing a Fitted Point Process Model

Simulate Neyman-Scott Process

The Strauss Point Process Model

Multidimensional Space-Time Point Pattern

Convert Line Segment Pattern to Another Unit of Length

Nearest neighbour distances in three dimensions

Extract.splitppp

Extract or Replace Sub-Patterns

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Lengths of Line Segments

Plot a three-dimensional point pattern

Spokes pattern of dummy points

Diagnostic Plots for Fitted Point Process Model

Simulate Baddeley-Silverman Cell Process

Pairwise distances between two different point patterns

Poisson Line Tessellation

Pair Correlation Function of Point Pattern

Extract List of Tiles in a Tessellation

Plot a List of Point Patterns

Methods for Three-Dimensional Box

Apply Vector Translation To Point Pattern

Window in Shape of Letter R

The Soft Core Point Process Model

Pairwise distances between two different three-dimensional point patterns

Test Whether a Window is Convex

Compute Areas of Tiles in a Tessellation

Estimate window from points alone

Generate N Uniform Random Points

Difference of Disc Areas

Hybrid Geyer Point Process Model

Test Whether An Object Is A Window

Compute Integral of Function Against Cumulative Distribution

Simulate Stratified Random Point Pattern

Spruces Point Pattern

Artificial Data Point Pattern

Local pair correlation function

Marks of a Line Segment Pattern

Place Points Evenly Along Specified Lines

Generate Poisson Point Pattern on Line Segments

Sufficient Statistic of Point Process Model

Weighted Histogram

Berman's Tests for Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Ord Interaction Process Family

The Lennard-Jones Potential

California Redwoods Point Pattern (Entire Dataset)

Exponential Energy Marks

Generate N Random Multitype Points

The Fiksel Interaction

Generic Pairwise Interaction model

Endpoints of Line Segment Pattern

Apply Vector Translation To Pixel Image

Saturated Pairwise Interaction model

Geyer's Saturation Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Data Sharpening of Point Pattern

Volume of an Object

Interactively Define a Polygon

K-function of a Three-Dimensional Point Pattern

Mark Correlation Integral

Plot a Colour Map

Estimate the J-function

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Update a Fitted Cluster Point Process Model

Convert and Compare Colours in Different Formats

Saturated Pairwise Interaction Point Process Family

Difference of Disc Areas

plot a Spatial Line Segment Pattern

plot a Spatial Point Pattern

Multitype K Function (i-to-any)

Residuals for Fitted Point Process Model

Simulate Gauss-Poisson Process

Bronze gradient filter data

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Apply Function to Every Neighbourhood in a Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Extract Subset of Signed or Vector Measure

Create a Point Matching

Convert Point Pattern to Pixel Image

Inhomogeneous Cross Type L Function

Perfect Simulation of the Strauss Process

Test Whether A Point Process Model is Marked

Multitype pair correlation function (cross-type)

Apply Vector Translation

Nearest neighbour distances

Union of Data and Dummy Points

Kernel Smoothed Intensity of Point Pattern

Simulation Envelopes of Summary Function

spatstat-deprecated

Deprecated spatstat functions

Generate Poisson Point Pattern in Three Dimensions

Print Brief Details of an Image

Plot a Signed or Vector-Valued Measure

Test Whether An Object Is A Fitted Point Process Model

Midpoints of Line Segment Pattern

Create a Tessellation

Generate Poisson Point Pattern

Generate a Quadrature Scheme from a Point Pattern

Subset of Quadrature Scheme

Generic Ord Interaction model

Aherne's hamster tumour data

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Find Largest Circle Inside Window

Rectangular grid of points

Interpret Fitted Model for Metropolis-Hastings Simulation.

Print a Quadrature Scheme

Dirichlet Tessellation of Point Pattern

Summary of a Point Pattern Dataset

Test Whether An Object Is Empty

Empty Space Function of a Three-Dimensional Point Pattern

Morphological Erosion

Circular Window

California Redwoods Point Pattern (Ripley's Subset)

Number of Points in a Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Smooth a Signed or Vector-Valued Measure

Intersect Infinite Straight Lines with a Window

Pine saplings in Finland.

Approximate a Polygon by a Simpler Polygon

Marked K-Function

Determine Initial State for Metropolis-Hastings Simulation.

Calculate four standard summary functions of a point pattern.

Hyper Data Frame

Pairwise distances

Create a Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

spatstat-package

The Spatstat Package

Cut margins from rectangle

Lansing Woods Point Pattern

Function Arrays for Spatial Patterns

Foxall's Distance Functions

rshift.splitppp

Randomly Shift a List of Point Patterns

Simulated Point Pattern

Diameter of an Object

Define Point Process Model for Metropolis-Hastings Simulation.

Multitype Nearest Neighbour Distance Function (i-to-j)

Summary of a List of Things

Superimpose Several Line Segment Patterns

Class of Line Segment Patterns

Print Progress Reports

Data and Code From JRSS Discussion Paper on Residuals

Tropical rain forest trees

Methods for Multi-Dimensional Box

Random Perturbation of a Point Pattern

Centroid of a window

matclust.estpcf

Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation

Simulate a Fitted Gibbs Point Process Model

Compute Fitted Effect of a Spatial Covariate in a Point Process Model

project2segment

Move Point To Nearest Line

The Multitype Hard Core Point Process Model

The Strauss / Hard Core Point Process Model

Multitype J Function (i-to-any)

Biological Cells Point Pattern

Random Re-Labelling of Point Pattern

Distance Map as a Function

Beta Ganglion Cells in Cat Retina

Make Periodic Copies of a Spatial Pattern

Test Whether Marks Are Present

Morishita Index Plot

plot a Spatial Quadrature Scheme

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Distance Between Two Point Patterns

Mark Connection Function

The Piecewise Constant Pairwise Interaction Point Process Model

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Lurking variable plot

Harkness-Isham ants' nests data

Analysis of Deviance for Spatial Logistic Regression Models

Test Whether A Point Pattern is Marked

Simulate from a Fitted Point Process Model

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Create a Pixel Image Object

Nonparametric Estimate of Spatially-Varying Relative Risk

crossdist.default

Pairwise distances between two different sets of points

Fit the Thomas Point Process by Minimum Contrast

Convert Data To Class ppp

Prediction from a Fitted Cluster Point Process Model

Point and Click Interface for Exploratory Analysis of Point Pattern

Infinite Straight Lines

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Convert to Pixel Image

Extract Quadrature Scheme Used to Fit a Point Process Model

Multi-Dimensional Box

Apply Affine Transformation To Window

Convert dataset to another unit of length

Convert Line Segment Pattern to Pixel Image

Safely Convert Point Pattern Window to Binary Mask

pairwise.family

Pairwise Interaction Process Family

Mark Correlation Function

Combine Function Value Tables

model.frame.ppm

Extract the Environment of a Point Process Model

plot a Fitted Point Process Model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Class of Quadrature Schemes

Contour plot of pixel image

Simulate systematic random point pattern

Locally Scaled K-function

Rotate a Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Multitype K Function (Cross-type)

Hutchings' Bramble Canes data

The Area Interaction Point Process Model

Identify Points in a Point Pattern

Chorley-Ribble Cancer Data

Simulate Matern Model I

Longleaf Pines Point Pattern

Geometrical Calculations for Multi-Dimensional Box

Expand Window By Factor

Plot a Pixel Image

Generate Poisson Point Pattern in Any Dimensions

Simulate Matern Model II

Diggle's Heather Data

Three-Dimensional Box

Nearest Neighbours Between Two Patterns

Identify Segments in a Line Segment Pattern

Convert Polygonal Region into Different Format

Kaplan-Meier and Reduced Sample Estimator using Histograms

Level Set of a Pixel Image

Galaxies in the Shapley Supercluster

Pair Correlation Function obtained from K Function

Name for Unit of Length

Number of Line Segments in a Line Segment Pattern

Extract Unique Points from a Spatial Point Pattern

Combine Two Line Segment Patterns

Simulate Thomas Process

Plot a tessellation

Simulate Matern Cluster Process

inforder.family

Infinite Order Interaction Family

Plot a Spatial Window

model.matrix.ppm

Extract Design Matrix from Point Process Model

Quadrature Scheme Based on Pixel Grid

Reduced Sample Estimator using Histogram Data

Loglikelihood of Spatial Logistic Regression

Superimpose Several Point Patterns

Inhomogeneous Cross K Function

Nearest Neighbour Clutter Removal

Set Covariance of a Window

New Zealand Trees Point Pattern

Generate N Uniform Random Points in Three Dimensions

Three Dimensional Point Pattern

spatstat-internal

Internal spatstat functions

Convert Window to Pixel Image

Predicted or Fitted Values from Spatial Logistic Regression

Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True

Evaluate Expression Involving Pixel Images

Update a Fitted Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Random Thinning

Swedish Pines Point Pattern

Class of Fitted Point Process Models

Print a Fitted Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

plot.hyperframe

Plot Entries in a Hyperframe

Prediction from a Fitted Point Process Model

Quadrat counting for a point pattern

Cross Validated Bandwidth Selection for Relative Risk Estimation

Fitted Probabilities for Spatial Logistic Regression

Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Apply Vector Translation To Line Segment Pattern

Sample Quantiles of Pixel Image

Marked Nearest Neighbour Distance Function

Randomly Shift a Point Pattern

Generate a Default Pattern of Dummy Points

Apply Gaussian Blur to a Pixel Image

Convert Data to Hyperframe

Print Brief Details of a Spatial Window

Generate N Uniform Random Points in Any Dimensions

Plot a fitted cluster point process

Pairwise distances in Three Dimensions

Determine Duplicated Points in a Spatial Point Pattern

Reduced Second Moment Measure

Convert Pixel Image to Another Unit of Length

Generate Multitype Poisson Point Pattern

Spatial Logistic Regression

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Border Region of a Window

Create a Line Segment Pattern

Rotate a Line Segment Pattern

Vertices of a Window

Generate grid of parallel lines with random displacement

bounding.box.xy

Convex Hull of Points

Cartesian Coordinates for a Pixel Raster

Humberside Data on Childhood Leukaemia and Lymphoma

Data Frames of Function Values

Generate N Uniform Random Points in a Disc

Print Brief Details of a Point Pattern Dataset

Find Line Segment Nearest to Each Point

Nearest Neighbour Distances in Any Dimensions

Read Point Pattern From Data File

Divide Image Into Sub-images

Rotate a Window

Crossing Points of Two Line Segment Patterns

Fit Point Process Model to Data

Class of Point Patterns

Extract Subset of Line Segment Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Methods for Multidimensional Space-Time Point Patterns

Basis for Harmonic Functions

Plot a List of Things

Apply Vector Translation To Window

Distance Map of Window

Nearest Neighbours in Any Dimensions

Spatial smoothing of observations at irregular points

Summary of a Line Segment Pattern Dataset

Set Control Parameters for Metropolis-Hastings Algorithm.

Plot a plotppm Object Created by plot.ppm

Estimate Variance of Summary Statistic by Subdivision

Apply Smoothing to Function Values

pairdist.default

Pairwise distances

Plot a Function Array

rescue.rectangle

Convert Window Back To Rectangle

Methods for three-dimensional point patterns

Interpolate a Pixel Image

Evaluate an Expression in a Function Table

Plot Function Values

Divide Point Pattern into Sub-patterns

Mosaic Random Field

Identify Pixelwise Maximum of Several Pixel Images

Perimeter Length of Window

Variance-Covariance Matrix for a Fitted Point Process Model

Summarizing a Quadrature Scheme

Delaunay Triangulation of Point Pattern

Compute Quadrature Weights Based on Grid Counts

Pixel Image Approximation of a Window

Extract or Replace Subset of a List of Things

Convert Data To Class psp

Convex Hull of Points

Estimate the empty space function F

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Nearest Neighbour Distance Function G

Extract Subset of Function Values

Distance to Boundary of Window

Connected components of an image or window

Collapse Several Function Tables into One

Geometrical Calculations for Three-Dimensional Box

Diameter of a Window

Convert Line Segment Pattern to Binary Pixel Mask

Apply Function to Image Broken Down by Factor

Extract Subset of Function Array

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Nearest neighbour

Extract or Replace Subset of Tessellation

Multitype Nearest Neighbour Distance Function (i-to-any)

Convert Pixel Image to Matrix or Array

Evaluate Expression Involving Functions

Area of Part of Disc

Berman-Huntington points and lines data

Hughes' Amacrine Cell Data

Convert Spatial Object to Pixel Image

plot.bermantest

Plot Result of Berman Test

Neighbourhood density function

Beta Ganglion Cells in Cat Retina, Old Version

Fry Plot of Point Pattern

Plot a Spatial Kolmogorov-Smirnov Test

Test Whether Points Are Inside A Window

Extract Original Data from a Fitted Point Process Model

Plot a Fitted Spatial Logistic Regression

Convert Data To Tessellation

Convert Point Pattern to Another Unit of Length

Method of Minimum Contrast

Coefficients of Fitted Point Process Model

Multitype L-function (cross-type)

methods.distfun

Methods for Distance Functions

Pair Correlation Function obtained from array of K functions

pppmatching.object

Class of Point Matchings

Randomly Shift a Line Segment Pattern

Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts

Pair Correlation Function

Summary of a Spatial Window

Simulate Simple Sequential Inhibition

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Urkiola Woods Point Pattern

Theoretical Distribution of Nearest Neighbour Distance

Compute Images of Constructed Covariates

Corners of a rectangle

Extract Dummy Points Used to Fit a Point Process Model

Point and Click Interface for Displaying a Point Pattern

summary.splitppp

Summary of a Split Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Generate Poisson Random Line Process

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Create a Window

Intersection, Union or Set Subtraction of Two Windows

Marks of a Point Pattern

Profile Maximum Pseudolikelihood

Divide Region into Quadrats

Plot a Simulation Envelope

Generate N Random Points

Pairwise distances

spatstat.options

Internal Options in Spatstat Package

Interaction Distance of a Point Process

Simulate a Fitted Cluster Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Simulation Envelopes of Summary Function for 3D Point Pattern